update github actions to new version and make tests pass again

.github/workflows/run-tests.yml

@@ -6,42 +6,60 @@ jobs:
  latest:
  runs-on: ubuntu-latest
  strategy:
+ fail-fast: false
  matrix:
- python-version: [3.6, 3.7, 3.8, 3.9]
+ python-version: ["3.9", "3.10", "3.11", "3.12"]
 
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v4
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install dependencies
  run: |
+ python -m venv --system-site-packages env
+ source env/bin/activate
  python -m pip install --upgrade pip
- pip install -r pip-requirements.txt
+ python -m pip install -r pip-requirements.txt
+ python --version
+ python -c 'import numpy; print(numpy.__version__)'
+ python -c 'import cython; print(cython.__version__)'
+ python ./setup.py develop
+ # python -m pip -vvv install -e .
+ # fails with "ModuleNotFoundError: No module named 'Cython'"
+ # running setup.py directly is just a workaround.
  - name: run tests
  run: |
- ./run-tests.py
+ source env/bin/activate
+ python run-tests.py --skip-setup
 
  other-os:
  runs-on: ${{ matrix.os }}
  strategy:
  matrix:
  os: [macos-latest, windows-latest]
- python-version: [3.8]
+ python-version: [3.12]
 
 # have to copy steps from above, as anchors are currently
 # not supported by github workflow (Jan 2020).
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v4
  - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v1
+ uses: actions/setup-python@v4
  with:
  python-version: ${{ matrix.python-version }}
  - name: Install dependencies
  run: |
  python -m pip install --upgrade pip
- pip install -r pip-requirements.txt
+ python -m pip install -r pip-requirements.txt
+ python --version
+ python -c 'import numpy; print(numpy.__version__)'
+ python -c 'import cython; print(cython.__version__)'
+ python ./setup.py develop
+ # python -m pip -vvv install -e .
+ # fails with "ModuleNotFoundError: No module named 'Cython'"
+ # running setup.py directly is just a workaround.
  - name: run tests
  run: |
- ./run-tests.py
+ python run-tests.py --skip-setup

pip-requirements.txt

@@ -2,7 +2,7 @@
 
 pycodestyle
 nose2
-cython>=0.18
+Cython>=0.18
 numpy>=1.8
 
 # required for building the docs

setup.py

@@ -42,7 +42,8 @@
  # does not work for python 2
  'numpy>=1.8', 'numpy>=1.9;python_version<"3.0"',
  'scipy', 'future', 'urllib3', 'numexpr',
- 'cython>=0.18', 'functools32;python_version<"3.0"'],
+ 'cython>=0.18', 'functools32;python_version<"3.0"',
+ 'packaging'],
  extras_require = {
  'h5 reader for openPMD support': ['h5py'],
  'sdf support for EPOCH reader': ['sdf'],